I have already done a lot of research on this problem.
I have already uninstalled and installed cygwin more than 5 times.
Done rebaseall everytime I installed it.
Checked for possible BLODA, I had notron antivirus, which I have removed.

As an aside, I tried posting this question to cygwin mailing list after subscribing to it. But my mail does not appear on the list. I suppose they want address to be munged and I have no clue how to do it. supposedly, they are treating it as a spam.
Any idea how I can post to the mailing list there.

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I am not able to put output of cygcheck and rebase as it becomes very big. Also, if i try to snip it, it does not accept it saying not proper formatting. I think i cant attach anything in stack overflow, so not sure what to do?
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Techie HelpNov 30 '12 at 11:08

The most likely reason for your email being rejected from the Cygwin mailing list is that it's not in plain text. How to fix that depends on your mail client, but Googling for "{mail client} plain text email" will help.
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me_andNov 30 '12 at 16:04

For large output files dumps, your best bet is to dump them onto your favourite online pastebin, then link to them.
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me_andNov 30 '12 at 16:08